mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
process CHECKM_LINEAGEWF {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::checkm-genome=1.1.3" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1' :
|
|
'quay.io/biocontainers/checkm-genome:1.1.3--py_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
val fasta_ext
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}") , emit: checkm_output
|
|
tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
checkm \\
|
|
lineage_wf \\
|
|
-t $task.cpus \\
|
|
-f ${prefix}.tsv \\
|
|
--tab_table \\
|
|
--pplacer_threads $task.cpus \\
|
|
-x $fasta_ext \\
|
|
$args \\
|
|
. \\
|
|
$prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
checkm: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|